def __init__(self, java_path="", max_threads=4, jar_path="", jar=None):
jar = "trimmomatic.jar" if jar is None else jar
JavaTool.__init__(self,
jar,
java_path=java_path,
max_threads=max_threads,
jar_path=jar_path,
max_memory=None,
timelog="trimmomatic.time.log")
def __init__(self,
java_path="",
max_threads=4,
jar_path="",
max_memory="1g"):
jar = "picard.jar MarkDuplicates"
JavaTool.__init__(self,
jar,
java_path=java_path,
max_threads=max_threads,
jar_path=jar_path,
max_memory=max_memory)
def __init__(self,
max_threads=4,
jar_path="",
jar="snpEff.jar",
max_memory="500m",
config_path=""):
JavaTool.__init__(self,
jar,
java_path="",
max_threads=max_threads,
jar_path=jar_path,
max_memory=max_memory)
self.config_path = config_path
def __init__(self,
java_path="",
max_threads=4,
jar_path="",
max_memory=None,
timelog=None):
JavaTool.__init__(self,
"GenomeAnalysisTK.jar -T AnalyzeCovariates",
java_path=java_path,
max_threads=max_threads,
jar_path=jar_path,
max_memory=max_memory,
timelog=timelog)
def __init__(self,
java_path="",
max_threads=4,
jar_path="",
max_memory=None,
timelog=None):
JavaTool.__init__(self,
"GenomeAnalysisTK.jar -T UnifiedGenotyper",
java_path=java_path,
max_threads=max_threads,
jar_path=jar_path,
max_memory=max_memory,
timelog=timelog)
def __init__(self,
java_path="",
max_threads=4,
jar_path="",
max_memory=None,
timelog=None):
JavaTool.__init__(self,
"GenomeAnalysisTK.jar -T VariantRecalibrator",
java_path=java_path,
max_threads=max_threads,
jar_path=jar_path,
max_memory=max_memory,
timelog=timelog)
def __init__(self,
java_path="",
max_threads=4,
jar_path="",
max_memory=None,
timelog="tool_time.log"):
JavaTool.__init__(self,
"GenomeAnalysisTK.jar -T SelectVariants",
java_path=java_path,
max_threads=max_threads,
jar_path=jar_path,
max_memory=max_memory,
timelog=timelog)
def __init__(self,
java_path="",
max_threads=4,
jar_path="",
max_memory="1g"):
#JavaTool.__init__(self, "CreateSequenceDictionary.jar", java_path=java_path, max_threads=max_threads,
# jar_path=jar_path, max_memory=max_memory)
JavaTool.__init__(self,
"picard.jar CreateSequenceDictionary",
java_path=java_path,
max_threads=max_threads,
jar_path=jar_path,
max_memory=max_memory)
def __init__(self,
java_path="",
max_threads=4,
jar_path="",
max_memory=None,
timelog=None):
JavaTool.__init__(
self,
"GenomeAnalysisTK.jar -T FastaAlternateReferenceMaker",
java_path=java_path,
max_threads=max_threads,
jar_path=jar_path,
max_memory=max_memory,
timelog=timelog)
def __init__(self,
java_path="",
max_threads=4,
jar_path="",
max_memory="1g"):
#JavaTool.__init__(self, "AddOrReplaceReadGroups.jar", java_path=java_path, max_threads=max_threads,
# jar_path=jar_path, max_memory=max_memory)
JavaTool.__init__(self,
"picard.jar AddOrReplaceReadGroups",
java_path=java_path,
max_threads=max_threads,
jar_path=jar_path,
max_memory=max_memory)
def __init__(self,
java_path="",
max_threads=4,
jar_path="",
max_memory=None,
timelog=None):
JavaTool.__init__(
self,
"GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.CatVariants",
java_path=java_path,
max_threads=max_threads,
jar_path=jar_path,
max_memory=max_memory,
timelog=timelog)
def __init__(self, java_path="", max_threads=4, jar_path="", max_memory=None, timelog=None):
JavaTool.__init__(self, "GenomeAnalysisTK.jar -T RealignerTargetCreator", java_path=java_path,
max_threads=max_threads, jar_path=jar_path, max_memory=max_memory,
timelog=timelog)
def __init__(self, java_path="", max_threads=4, jar_path="", max_memory="1g"):
jar = "AddOrReplaceReadGroups.jar"
JavaTool.__init__(self, jar, java_path=java_path, max_threads=max_threads,
jar_path=jar_path, max_memory=max_memory)
def __init__(self, java_path="", max_threads=4, jar_path="", max_memory="1g"):
jar = "CreateSequenceDictionary.jar"
JavaTool.__init__(self, jar, java_path=java_path, max_threads=max_threads,
jar_path=jar_path, max_memory=max_memory)